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The gut microbiota—a clinical perspective on lessons learned


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The gut microbiota—a clinical perspective on lessons learned

  1. 1. FOCUS ON GUT MICROBIOTAOPINION certainly, other diseases, including some forms of colorectal cancer, have a micro-The gut microbiota—a clinical bial aetiology.3 Second, the story showed the value of traditional culture-basedperspective on lessons learned techniques and the wisdom of working with model organisms to understandFergus Shanahan disease mechanisms. Third, after decades of missing a trans­ issible cause of peptic mAbstract | Once considered obscure and largely ignored by microbiologists, the human ulceration, the discovery exposed the limi-microbiota has moved centre-stage in biology. The gut microbiota is now a focus of tations of ‘risk factor epidemiology’ withoutdisparate research disciplines, with its contributions to health and disease ready for taking into account the disease mecha-translation to clinical medicine. The changing composition of the microbiota is linked nisms, whilst it also highlighted the impor-with changes in human behaviour and the rising prevalence of immunoallergic and tance of thinking across the boundariesmetabolic disorders. The microbiota is both a target for drug therapy and a repository of traditional research disciplines to solvefor drug discovery. Its secrets promise the realization of personalized medicine and important biological problems. Finally, asnutrition, and will change and improve conventional dietary management. the prevalence of H. pylori was in decline in developed countries long before its exist-Shanahan, F. Nat. Rev. Gastroenterol. Hepatol. 9, 609–614 (2012); published online 14 August 2012; ence was known, the story poses importantdoi:10.1038/nrgastro.2012.145 clinical questions regarding the changing nature of the human microbiota.Introduction This judgement from one so closelyFew developments in biology promise as linked with the human genome is par- Microbiota change—disease riskmuch to the advancement of medicine as the ticularly pertinent to the human micro- An abrupt rise in the frequency of immuno­exploration of the indigenous human micro- bia l environ­ ent. Gast rointest ina l m allergic disorders, such as IBD and asthma,biota. Since the publication of historic exper- patho­ hysiology cannot be conclusively p occurs with socioeconomic develop-iments performed with germ-free animals, examined outside the context of the ment. This association has been attrib-it has been evident that the microbiota is relation­ship with our microbial selves. Over uted to reduced environmental exposurea source of trophic, metabolic and protec- the past decade, a convergence of research to microbes (the hygiene hypothesis), buttive signals, from which the host benefits. interest from disparate cognitive disciplines more accurately might be related to changesHost–microbe interactions are now known has greatly enhanced the understanding of in microbial colonization during the earliestto be bidirectional and disturb­ances of these the human microbiota and of host–microbe stages of life, when the immune system isinteractions contribute to gastrointestinal interactions. Progress has been acceler- maturing. Microbial signalling is required,and extraintestinal disorders. Mining host– ated by metagenomics, which combines not only for mucosal homeo­ tasis, but also smicrobe signalling has long promised much, high-throughput DNA sequencing and for full development of extra­ ntestinal ibut several pivotal discoveries and advances computational methods to define the com- systems, including the brain–gut axisin mol­ cular microbiology are now poised e position of complex microbial communities and the immune response. Loss of ances-for translation to clinical medicine. This without needing to culture the constituents. tral organisms, such as H. pylori and hel-article focuses on the clinical implications Microbial genes (the microbiome) numeri- minths, is associated with socio­ conomic eof advances in human microbial ecology; the cally exceed those of the human genome development, and is a risk factor for certainlessons learned extend beyond the gut and by 100‑fold, and microbes from the three diseases. Reduced microbial diversityare germane to all clinical specialties. domains of life (Bacteria, Archaea and accompanies many gastrointestinal and Eukarya), along with viruses, are repre- extraintestinal disorders, but reduced levelsFeatures of the gut microbiota sented within the normal human micro­ of specific organisms, such as LactobacilliIn 2007, J. Craig Venter wrote that “Without biota, including species that were unknown spp., Bifidobacterium spp., Akkermansiaunderstanding the environment in which until recently.2,3 Work from various labora- muciniphilia and Faecalibacterium praus-cells or species exist, life cannot be under- tories has revealed the complexity, majesty nitzii, might confer a particular risk ofstood. An organism’s environment is and diversity of the microbiota (Table 1).2,3 developing IBD.2–5ultimately as unique as its genetic code.”1 The discovery of Helicobacter pylori by The earlier the exposure to a modern clinicians refusing to accept dogma is argu- lifestyle in a developed country, the greater ably the field’s greatest success story and is the risk of disease. This finding is con-Competing interests has yielded several lessons of continuing sistent with the onset of many immuno­The author declares associations with the clinical relevance. First, it showed that the allergic disorders in adolescence or earlyfollowing companies: Alimentary Health,GlaxoSmithKline, Procter & Gamble. See the solution to some diseases cannot be found adulthood, and is confirmed by migrationarticle online for full details of the relationships. by focussing exclusively on the host. Almost studies5 (Figure 1). Many of the elements ofNATURE REVIEWS | GASTROENTEROLOGY & HEPATOLOGY VOLUME 9  |  OCTOBER 2012  |  609 © 2012 Macmillan Publishers Limited. All rights reserved
  2. 2. PERSPECTIVES Table 1 | Overview of the gut microbiota* Feature Comment High diversity and density Loss of microbial diversity predisposes to pathogenic infections and is linked with several immunoallergic and metabolic disorders Individuality Variation arises at species and strain levels with limited variability at phylum level; members of two phyla (Firmicutes and Bacteroidetes) contribute to ~90% of the species in the distal gut Maternal transmission Colonization at birth is influenced by mode of delivery (vaginal versus caesarean section) Age-dependent variability Rapid diversification during infancy influenced by diet and environment, including antibiotics, reaching relative stability with idiosyncrasy in adulthood, and changing in the elderly depending on physiological status, diet, drugs and morbidity Variation over long axis of gut After the oral cavity, complexity and numbers increase distally Variation over cross-sectional The aerobe:anaerobe ratio is greater at the mucosal surface than at the lumen axis of gut Resilience The microbiota tends to return to normal after antibiotic challenge, but some strains might be eliminated, particularly after repeated or prolonged antibiotic exposure, with the greatest effect in infancy Plasticity and adaptability On a background of relative stability, there are continual variations in metabolic behaviour and composition depending on diet, other lifestyle variables and disease Host–microbe interactions Bidirectional; microbial, immunoinflammatory and metabolic cascades are interactive Spatial segregation and Microbes have restricted access to the small intestinal epithelia because of host-derived factors, such as the antibacterial compartmentalization lectin RegIII-γ; and in the colon, the structure of the inner layer of colonic mucin ensures that it is microbe-free; if commensal organisms penetrate the mucosa they are restricted from the systemic circulation by a gatekeeper effect of the mesenteric lymph node Experimental transferrable ‘Colitogenic’ microbiota from animal models of colitis can transfer disease to naive genetically wild-type recipients; microbiota transplants of microbiota have similarly revealed transferrable metabolic phenotypes *Source material reviewed, in part, in references 2 and 3.a modern lifestyle in a developed country metabolites that promote atherosclerosis the gut, including diabetes, obesity andinfluence the composition of the indigenous after absorption and hepatic metabolism.10 related complications (Figure 3). The firstmicrobiota, disturbances of which have This finding has brought personalized intersection of microbes, immunity andbeen reported in several diseases of devel- nutrition a step closer to reality but, as dis- metabolism arises at the intestinal epithe-oped society. The most obvious lifestyle or cussed below, is only one part of an unfold- lium. The immune and metabolic functionsenvironmental modifier of the microbiota ing story linking the microbiota with both of the epithelium (for example, IgA releaseis increased antibiotic exposure, particu- immunoinflammatory and metabolic and lipid absorption, respectively) are func-larly in infancy, which has been linked with signalling in the host. tionally interconnected and inversely regu-an increased risk of IBD in childhood in lated.14 IgA influences the composition ofpopulation-based studies. 6,7 Early anti­ Microbe–host signalling the commensal microbiota and, if deficient,biotic exposure might also increase the risk Microbe–host signalling is reciprocal, and the commensal bacteria drive interferon-of asthma, and perhaps even metabolic and occurs at several levels: with the immune dependent expression of genes controllingobesity-related disease, in later life. system; with host metabolic processes; immunity, at the expense of those regulat- Dietary intake is another prominent and with the enteric nervous system and ing metabolism. This effect might contrib-modifier of the microbiota (Figure 2). For brain–gut axis. Interdependency within ute to lipid malabsorption in some forms ofexample, dietary polysaccharides and oligo­ this network is shown by the mutual regula- immune deficiency.saccharides, including fibres, are bifido- tion of the microbiota and immune system. By contrast, disturbed host metabolismgenic (that is, they enhance the growth of Microbial signalling is required for immune with excess fat storage might arise frombeneficial bifidobacteria), whereas micro- development and homeostasis, whereas defects in innate immunity. Experimentalbial compositional changes have been an intact immune system is necessary for mice lacking Toll-like receptor (TLR)5, thelinked with high levels of dietary fat, iron maintenance of a healthy microbiota. A immunosensory receptor for microbialand protein (casein).8 Of note, increased depleted microbiota might result in an flagellin, develop obesity and insulin resist-consumption of dietary fat in Japan, partic- immune deficit, whereas defects in innate ance.12 This result seems to be attributableularly animal fat and n‑6 polyunsaturated immunity lead to an altered gut micro- to alterations in the composition of the gutfatty acids, has been closely correlated with biota, which might transfer inflammatory microbiota, which induce proinflamma-increases in the incidence of both Crohn’s and metabolic disease phenotypes upon tory cytokines, leading to desensitization ofdisease and ulcerative colitis.9 faecal transplantation.11–13 insulin receptor signalling with consequent Dietary modification of the intestinal Interactions between inflammatory and hyperphagia and weight gain. Defects at themicrobiota has also been linked with meta- metabolic cascades are well established. level of the inflammasomes are also associ-bolic and cardiovascular disease. A striking Modulation of both of these processes ated with changes in microbial composi-example is the discovery of a microbial- by the microbiota has added an intrigu- tion, activation of inflammatory cascadesdependent pathway for the metabolism ing layer of complexity, with therapeutic and progression of metabolic disease.13,15,16of dietary phospholipids that generates implications for several diseases beyond Inflammasomes, as discussed later, are610  |  OCTOBER 2012  |  VOLUME 9 © 2012 Macmillan Publishers Limited. All rights reserved
  3. 3. FOCUS ON GUT MICROBIOTAintracellular sensors of microbial-induced Migration from developing (low-risk) regions to developed (high-risk) regionsdamage, but also sense metabolic disturb­ance in the host and might determine whysome patients with obesity are metaboli-cally normal and why others progress tomulti­ rgan complications, including steato­ ohepatitis and insulin resistance. 15,16 The High-riskmicrobiota might confound host metab­ High-risk regionolism by additional mechanisms (Figure 3). region Low-riskHowever, the microbiota also intersects host regionsmetabolism and inflammatory tone by regu-lating fatty-acid composition within fat tissue,the bioactivity of which influences the pro-duction of inflammatory cytokines.17 Thus,the microbiota has a regulatory influence onboth fat quantity and quality in the host. As microbial, inflammatory and meta-bolic signalling pathways are interlinkedand each limb of this triangular network isinfluenced by diet, it follows that identifi-cation and manipulation of the microbialsignals and/or alteration of the inflam-matory response offer new therapeutic Age at time of migrationadjuncts to the management of obesity-related disease. The molecular detailsunderpinning this prospect have beenaddressed elsewhere,8 and proof of princi- Risk of acquiring disease of new worldple for an improved metabolic outcome by Figure 1 | Migration and disease risk. Migration studies confirm that lifestyle factors exert theirtargeted manipulation of gut microbiota in influence at the earliest stages of life (when the microbiota is becoming established and whilstdiet-induced obesity has been established.18 the immune system is maturing). The risk of various immunoallergic disorders is greater the earlier a migrant moves from a region of low-risk (‘developing’ socioeconomically) to one of high-The sensory conundrum risk (developed) and is low if they migrate in later life.What defines a commensal and how doesthe host distinguish harmless commensalsfrom dangerous or opportunistic patho- against reflux-associated complications, host.19 Whether other commensals deploygens? The distinction is not always clear, including metaplasia and neoplasia at the symbiosis-associated molecular patternseven at a clinical level. The simplest answer gastro­ sophageal junction, in later life. e is unclear, but the host has an intracellularis that all commensals probably have patho- How does the host interpret the micro- surveillance system to detect danger withingenic potential, depending on the context bial environment in terms of risk and the microbiota and to respond and maintainand host susceptibility, and some organisms benefit or what are traditionally referred compositional equilibrium.might be both beneficial and hazardous. For to as pathogens versus commensals? As Intracellular inflammasomes are multi­premature babies, colonization with other- the molecular patterns involved in recog- protein complexes, partly comprised ofwise harmless commensals before optimal nition of pathogens are also expressed by Nod-like receptors (NLRs), which sensedevelopment of immunity and mucosal nonpathogenic microbes, detection is only exogenous or endogenous stress or damage.barrier function poses a pathogenic threat. part of the process. The response decision The epithelium mobilizes the NLRP6Risk and benefit are also well represented is complex and seems to be based partly inflammasome in response to pathogenicin the H. pylori story, 3 with some clini- on specific inputs or symbiosis-associated components of the microbiota and triggerscians taking the view that ‘the only good molecular patterns from the microbiota 19 a cascade of events including: activationH. pylori is a dead H. pylori’. However, the and partly by sensing danger or damage- of caspase 1; conversion of pro­ nterleukin ioutcome of the Helicobacter–host inter- associated molecular patterns by epithe- IL‑18 to mature IL‑18; recruitment ofaction varies depending on the bacterial lial and other host cells 13 (Figure 4). An γ‑interferon-producing NK and T cells;strain, the host susceptibility and the age example of the former is the production and enhanced bacteriocidal activity of localof the host. Acquired in childhood, with a of an immunomodulatory polysaccharide macrophages.13 This inflammasome mobi-latent period of apparent health, H. pylori (polysaccharide A) by Bacteroides fragilis. In lization has a conditioning influence on themight cause peptic ulceration in adulthood contrast to other TLR2 ligands that promote composition of the gut microbiota, whichin some individuals, lymphoma in others clearance of pathogens, poly­ accharide A s becomes evident when NLRP6 is defi-and gastric cancer at a later age. By contrast, signals though TLR2 on regulatory T cells cient and the commensal bacteria becomethe same organism might confer protec- and suppresses T‑helper 17 effector cells, colito­ enic. Intestinal macrophages and gtion against asthma and possibly infections thereby avoiding an adverse immune dendritic cells have also been reported toin early life, and almost certainly protects response and favouring colonization of the have divergent responses to commensalsNATURE REVIEWS | GASTROENTEROLOGY HEPATOLOGY VOLUME 9  |  OCTOBER 2012  |  611 © 2012 Macmillan Publishers Limited. All rights reserved
  4. 4. PERSPECTIVES exposure to bacteria in the distal gut, an increasing list of drugs and other xeno­ biotics are substrates for bacterial enzymes and might arrive at the distal gut because ■ Smaller family size of delayed release formulations or after ■ Delayed infections Antibiotics/ biliary excretion. This delay might result vaccinations in metabolites with more or less activity, aHygiene andwater quality desirable example of the former being the release of aminosalicylate from the parent prodrug, sulphasalazine, whereas a classic example of the latter is microbial action on Microbiota Metabolic signalling digoxin. In other instances, toxins might be Lifestyle (early life) generated by microbial enzymatic action on drugs. A particularly informative example of the clinical effect of bacterial action on drugs has been shown in the case of Immune the colon cancer chemotherapeutic agent priming and inflammatory CPT‑11.22 After parenteral administration, signalling this drug is activated in vivo to generate the antineoplastic topoisomerase I toxin and is inactivated by glucuronidation in the liver, after which it arrives in the intestine by■ Diet and nutrition Urban life biliary excretion, where it is reactivated by■ Cooking and refrigeration bacterial glucuronidase. This process leadsFigure 2 | Lifestyle, microbiota and disease. The link between the elements of a modern lifestyle to dose-limiting diarrhoea, a problem thatin developed countries and risk of immune and metabolic disorders in later life might be throughan influence on the microbiota, particularly in infancy. Microbial, immune and metabolic can be circumvented using inhibitors thatsignalling events are interactive. are specific to the bacterial enzyme. Thus, the microbiota metabolizes some drugs and is a target for others.a b Mining the microbiota Mankind has exploited microbes with Microbiota Inflammatory tone ingenuity, from cleaning up oil slicks to production of monoclonal antibodies and Satiety, life-saving drugs. New therapeutic oppor- behaviour tunities arise as the molecular basis of host–microbe interactions unfold. These Diet include mining the microbiota for bio­ active compounds that might be formu-Immunity Metabolism lated as functional food ingredients or novel drugs (Table 2). The diversity of microbial metabolites Bioavailability storage of dietary nutrients and signalling molecules is testimony to theFigure 3 | A signalling internet a | Diet influences each component of a triangular network of richness of the microbiota as a repositorysignalling among the microbiota, host immunity and host metabolism. b | Mechanisms by which for drug discovery, but the pressing needthe microbiota influences host metabolism include: harvest of energy from dietary nutrients, for exploring this avenue is perhaps bestproduction of short-chain fatty acids (which signal via G protein-coupled receptors expressed by illustrated by increasing bacterial resist-the epithelium), and promotion of lipid storage in adipose tissue by suppressing fasting-induced ance from overuse of antibiotics and dimin-adipocyte factor, an inhibitor of lipoprotein lipase; modification of satiety and behaviour by ished pharmaceutical research.23 Concernssignalling through the brain–gut–microbe axis; and influencing the host’s inflammatory tone, about the long-term consequences of anti­including the ratio of proinflammatory and anti-inflammatory cytokines. bacterial action on the commensal micro- biota also call for agents with a narrowerversus pathogens, which are driven by the promise new therapeutic targets. Failure of spectrum of activity. An approach to theseNLRC4 inflammasome.20 the checkpoints for modifying the response problems is shown by the discovery that a Once an antimicrobial immune response to microbes might underpin or contribute Bacillus thuringiensis strain, isolated fromis launched, the host must determine the to chronicity of inflammatory disease.21 human faeces, produces thuricin CD, ascale of the threat and adapt accordingly potent anti­ icrobial peptide with narrow- mto limit inflammatory collateral damage. The ‘drugable’ microbiota spectrum efficacy against Clostridium dif-The molecular mechanisms by which this Although most drugs are absorbed in the ficile. This peptide is a naturally occurring,effect is achieved are becoming clear and upper gastrointestinal tract with little potential adjunct to existing antibiotics, of612  |  OCTOBER 2012  |  VOLUME 9 © 2012 Macmillan Publishers Limited. All rights reserved
  5. 5. FOCUS ON GUT MICROBIOTAcomparable efficacy, but with little resist- Commensal bacteria Pathogensance evident to date. More importantly, ?unlike antibiotics currently used againstC. difficile, thuricin CD has a narrow spec-trum of activity without collateral damageto the commensal microbiota.24Rebooting the systemClinicians often make a therapeutic leapbefore basic science catches up, the storyof H. pylori and peptic ulceration being Microbial factors Host factors Contextone example. Faecal microbial transplanta- Symbiosis-associated Damage-associated Wrong place at wrong timetion is an old remedy undergoing a resur- molecular patterns (SAMPS) molecular patterns (DAMPS) or host susceptibilitygence of interest because of promisingresults in various conditions, particularlyC. difficile-associated disease (CDAD). The TLR2problem of CDAD has escalated becauseof increasing antibiotic resistance, emer-gence of an epidemic hypervirulent strain(NAP1/B1/027) and recurrence rates of Mucosal Born too soon TREG cell Inflammasome —premature babyabout 20–25%.25 Curiously, the appendixmight act as a sanctuary for the resident Figure 4 | The sensory conundrum—friend or foe? The distinction between a harmlessmicrobiota that protects against C. difficile commensal and a potential pathogen occurs at different levels. Microbial factors: although the immune system does not express specific receptors to discriminate pathogens fromrecurrence, with increased rates of recur- commensals, some microbes produce molecules that act directly on regulatory T cells thatrence reported in patients who have had promote colonization by the organism. Host factors: epithelial inflammasomes are multiproteinan appendicectomy.26 It has been suggested intracellular sensors of cellular stress or damage that activate an immune response, therebythat the appendix might be both a locus of modifying the composition of the microbiota. Context: the host will respond to any commensalmucosal lymphoid tissue and a reservoir of found in the wrong place at the wrong time; for example, premature babies are colonized withnormal microbiota, from which the colon commensals that have pathogenic potential because the mucosal barrier, immune function andcan be re-populated to restore homeostasis blood–brain barrier are not yet completely developed.after challenge from antibiotics, disease andperhaps phage viruses. Different centres have wide variability Table 2 | Microbial activity translated to drug discovery or to functional foods 4,24,33–37concerning the acquisition, storage, prepa- Bacterial action Potential drug category Representative examplesration and mode of administration of faecal Microbe–microbe Antimicrobial (bacteriocin) Lactococcus lactis and Bacillus thuringiensis-derivedmaterial to patients, although a standard- signalling broad and narrow-spectrum bacteriocins againstized preparation and protocol has been Clostridium difficiledescribed.27 Critics claim that the bacterial Microbe–host Anti-inflammatory: Protective in experimental models of IBDcomponents of the administered material signalling Bacteroides fragilis- derived anti-inflammatoryshould be well defined and their interac- polysaccharide antigen;tions with other microbes established prior Lactobacillus-derived cellto making this therapy a routine practice. wall peptideOthers raise safety concerns, which will Microbe–host Cytoprotective Inhibition of cytokine-induced epithelial cell apoptosisincrease as faecal microbial transplantation signalling by a probiotic (Lactobacillus rhamnosus)-derived soluble protein acting as an epidermal growth factorbecomes more widespread or is applied to receptor agonistless serious or trivial conditions. Concern Microbe–host Analgesic Probiotic-derived analgesic effect in experimentalmight even become crisis if reports linking signalling functional bowel disorderspecific bacteria with colorectal cancer Microbial Vitamins and short-chain Short-chain fatty acids, conjugated linoleic acidare replicated and if the risk of cancer is metabolism fatty acidsshown to be transferrable.3 An alternative Genetically Delivery of vaccines or Reversal of autoimmune diabetes with L. lactisstrategy now underway in several centres modified bioactive agents to gut engineered to deliver proinsulin and IL‑10; treatmentis to define the minimal microbiota, that organisms of colitis with Bacteroides ovatus engineered tois, the combination(s) of strains sufficient secrete TGF‑β1 under control of dietary xylanto safely confer protection against recur-rence of CDAD and which can be char-acterized, stored and safely prepared for probiotics and pharmabiotics, in CDAD and Conclusionshuman administration without the risk of other disorders, have been addressed else- Helpful recommendations for fillinghuman–human disease transmission. where, the most important lesson being the persisting gaps in our knowledge of More nuanced approaches to mimic the need to match the selection of the probiotic host–microbe interactions in healthnormal microbiota, including prebiotics, strain with the clinical indication.28 and disease have been offered by severalNATURE REVIEWS | GASTROENTEROLOGY HEPATOLOGY VOLUME 9  |  OCTOBER 2012  |  613 © 2012 Macmillan Publishers Limited. All rights reserved
  6. 6. PERSPECTIVES 3. Cho, I. Blaser, M. J. The human microbiome: intestinal defense. Nat. Immunol. 13, 449–456investigators.3,29 The clinical benefits from at the interface of health and disease. Nat. Rev. (2012).exploring the microbiota should drive the Genet. 13, 260–270 (2012). 21. Blander, J. M. Sander, L. E. Beyond patternresearch, and although an extensive list of 4. Shanahan, F. The gut microbiota in 2011: recognition: five immune checkpoints for scalingpriorities remains, the benefits will include Translating the microbiota to medicine. Nat. Rev. the microbial threat. Nat. Rev. Immunol. 12, Gastroenterol. Hepatol. 9, 72–74 (2012). 215–225 (2012).the following. First, greater exploration of 5. Bernstein, C. N. Shanahan, F. Disorders of a 22. Wallace, B. D. et al. Alleviating cancer drugthe diversity and variation of the human modern lifestyle: reconciling the epidemiology toxicity by inhibiting a bacterial enzyme. 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Divergent metabolic 36. Hamady, Z. Z. et al. Treatment of colitis with aPharmabiotic Centre, University College Cork, outcomes arising from targeted manipulation of commensal gut bacterium engineered toNational University of Ireland, Biosciences the gut microbiota in diet-induced obesity. Gut secrete human TGF‑β1 under control of dietaryBuilding, College Road, Cork, Ireland. zylan 1. Inflamm. Bowel Dis. 17, 1925– gutjnl-2011-300705. (2011). 19. Round, J. L. et al. The Toll-like receptor 2 37. Shanahan, F. Gut microbes: from bugs to drugs.1. Venter, J. C. A Life Decoded. 3 (Penguin, Allen pathway establishes colonization by a Am. J. Gastroenterol. 105, 275–279 (2010). Lane, London, 2007). commensal of the human microbiota. Science2. Clemente, J. C., Ursell, L. K., Parfrey, L. W. 332, 974–977 (2011). Acknowledgements Knight, R. The impact of the gut microbiota on 20. Franchi, L. et al. NLRC-driven production of IL‑1β F. Shanahan is supported, in part, by Science human health: an integrative view. Cell 148, discriminates between pathogenic and Foundation Ireland, in the form of a centre grant: the 1258–1270 (2012). commensal bacteria and promotes host Alimentary Pharmabiotic Centre.614  |  OCTOBER 2012  |  VOLUME 9 © 2012 Macmillan Publishers Limited. All rights reserved